It's the same reason pasta water foams when you cook it; the starch and proteins are released into the water and cause the bubbles to sort become more pliable and "stretchy", preventing them from immediately bursting when they reach the surface (as regular boiling water does). Really, it's not harmful and will not affect the flavor or texture of the chowder. When the soup is removed from the heat and stirred, the bubbles will redistribute and "pop". That said, there's no reason why you can't skim it off if it bothers you or, worse, boils over onto your stove.
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